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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
4dfk 0L5 DNA polymerase I, thermostable 2.7.7.7

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 1.457
4df8 0L4DNA polymerase I, thermostable 2.7.7.7 1.054
1qsy DDSDNA polymerase I, thermostable 2.7.7.7 0.924
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 0.913
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.869
4dtj TTPDNA-directed DNA polymerase / 0.869
4dtp DGTDNA-directed DNA polymerase / 0.864
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 0.856
4fk4 DGTDNA-directed DNA polymerase / 0.845
4fj5 DTPDNA-directed DNA polymerase / 0.834
4khy TTPDNA-directed DNA polymerase / 0.828
3ne6 DCPDNA-directed DNA polymerase / 0.823
4fjl DGTDNA-directed DNA polymerase / 0.810
3lzj CTPDNA-directed DNA polymerase / 0.807
4m42 ATPDNA-directed DNA polymerase / 0.805
4dtx TTPDNA-directed DNA polymerase / 0.804
4m3x ATPDNA-directed DNA polymerase / 0.801
4fjj TTPDNA-directed DNA polymerase / 0.799
3sup DCPDNA-directed DNA polymerase / 0.795
4m3t ATPDNA-directed DNA polymerase / 0.786
3t3f N5PDNA polymerase I, thermostable 2.7.7.7 0.784
4fjh DGTDNA-directed DNA polymerase / 0.774
4fjm DCPDNA-directed DNA polymerase / 0.771
4xj4 3ATCyclic GMP-AMP synthase / 0.747
1cjv DADAdenylate cyclase type 2 / 0.744
1cjv DADAdenylate cyclase type 5 / 0.744
4dto DCPDNA-directed DNA polymerase / 0.741
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.740
3g6x DGTDNA polymerase iota 2.7.7.7 0.733
4dtm DCPDNA-directed DNA polymerase / 0.732
2q66 ATPPoly(A) polymerase 2.7.7.19 0.730
2b51 UTPRNA editing complex protein MP57 / 0.726
3au2 DGTDNA polymerase beta family (X family) / 0.718
3q23 G2PVirion DNA-directed RNA polymerase / 0.717
1xbt TTPThymidine kinase, cytosolic 2.7.1.21 0.714
3hiy UTPUncharacterized protein / 0.709
4k97 ATPCyclic GMP-AMP synthase / 0.708
4xj3 GTPCyclic GMP-AMP synthase / 0.707
3w2w ATPCRISPR system Cmr subunit Cmr2 / 0.706
4u03 GTPCyclic GMP-AMP synthase / 0.699
2b56 UTPRNA editing complex protein MP57 / 0.696
3wbz ATPtRNA(His) guanylyltransferase {ECO:0000256|PIRNR:PIRNR028980} / 0.691
1r89 CTPCCA-adding enzyme 2.7.7.72 0.683
2q0d ATPPoly(A) polymerase, putative / 0.683
4tyq AP5Adenylate kinase / 0.682
5i4n ATPTyrosine-protein kinase JAK2 / 0.678
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.677
4kgm ATPUncharacterized protein / 0.676
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.673
1r8c UTPCCA-adding enzyme 2.7.7.72 0.672
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.671
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.671
4fvq ATPTyrosine-protein kinase JAK2 / 0.668
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.662
4yl2 FMNLactate oxidase / 0.660
2rgx AP5Adenylate kinase / 0.659
5a2w AGSMitochondrial poly(A) polymerase / 0.658
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.656
1fmw ATPMyosin-2 heavy chain / 0.655
1qss DG3DNA polymerase I, thermostable 2.7.7.7 0.654
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.653
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.652
1a8r GTPGTP cyclohydrolase 1 3.5.4.16 0.650
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.650